Why do some dogs have two different colored eyes?

     The answer to this question is hidden in the Melanin.That is a pigment that is responsible for eye,skin and hair color in all animals.The process Mitosis by which the genes from their parents that has different eye colors most probably blue,green or golden join together and their product has two eyes of different colors.At the time of birth every single puppy has light blue eyes and the color changes as they grow up so it is also possible that because of the difference in amount of Pigment one eye color appears different than the other.
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